Who's to say then that Black Widow's not a liability too since she could still easily be bought out by the opposition, whomever that may be. Hell, they might even play with that idea a bit in Winter Soldier. But regardless, the Director of SHIELD apparently trusts her enough to keep her on board despite her questionable background that was completely devoid of mind control.

Speaking of mind control...

I would hope that Fury recognizes the circumstances of Barton's sudden 'mental weakness'. Which in reality was nothing like getting drunk, and nothing like a lapse in good judgement. We are talking about a cosmic level device of alien origin that is capable of COMPLETELY ENSLAVING AN INDIVIDUAL TO THE USER'S WILL. Fury even saw the process with his very own eye. Legal systems probably won't recognize alien mind slave devices, but Fury's whole agenda in Avengers was to be prepared for such outlandish situations. And guess who's pulling the strings here?

Regardless of what the legal systems are like in our world our theirs' I highly doubt that Fury would let Barton go on trial for such a thing, even if the World Council themselves ordered it. Fury cuts corners to fit his sense of justice, not a sense of legal process. For goodness sake's he shot down one of his own planes because he disagreed with the plan.

So unless they cut out Fury's control or bastardize his character, we won't be seeing Barton on trial or imprisoned. It will be swept under the rug, much like many of SHIELD's operations. They are the epitome of shadow agency and I very much believe they can completely and will completely reprieve Barton of any perceived war crimes.